OxyCalc software for oxygen estimates from blood vessels: MATLAB and Windows standalone version.
'OX-CALC - Oxygen distribution tool. Version 1.1. Authors: Dr. David Robert Grimes & Dr. Daniel R. Warren. This code allows the estimation of tissue oxygen from known vessel networks from the kernel method outlined here -http://rsif.royalsocietypublishing.org/content/13/116/20160070 - Code presented as is, and users are welcome to edit as desired.
Queries: E-mail davidrobert.grimes@oncology.ox.ac.uk / grimesd2@gmail.com or @drg1985.
Please cite as: Estimating oxygen distribution from vasculature in three-dimensional tumour tissue David Robert Grimes, Pavitra Kannan, Daniel R. Warren, Bostjan Markelc, Russell Bates, Ruth Muschel, Mike Partridge. J. R. Soc. Interface 2016 13 20160070; DOI: 10.1098/rsif.2016.0070.'
MATLAB instructions: Run the .m file in MATLAB, and follow the onscreen instructions. Select a vessel network file (.txt extension - samples are included in this repository from both Grimes et al and the work of Timothy Secomb and colleagues (see http://physiology.arizona.edu/people/secomb/greens for more information).
Windows Standalone: Run the .exe which will automatically install the MATLAB runtime if required. Follow onscreen instructions.